4,109 research outputs found
Simulation of reaction-diffusion processes in three dimensions using CUDA
Numerical solution of reaction-diffusion equations in three dimensions is one
of the most challenging applied mathematical problems. Since these simulations
are very time consuming, any ideas and strategies aiming at the reduction of
CPU time are important topics of research. A general and robust idea is the
parallelization of source codes/programs. Recently, the technological
development of graphics hardware created a possibility to use desktop video
cards to solve numerically intensive problems. We present a powerful parallel
computing framework to solve reaction-diffusion equations numerically using the
Graphics Processing Units (GPUs) with CUDA. Four different reaction-diffusion
problems, (i) diffusion of chemically inert compound, (ii) Turing pattern
formation, (iii) phase separation in the wake of a moving diffusion front and
(iv) air pollution dispersion were solved, and additionally both the Shared
method and the Moving Tiles method were tested. Our results show that parallel
implementation achieves typical acceleration values in the order of 5-40 times
compared to CPU using a single-threaded implementation on a 2.8 GHz desktop
computer.Comment: 8 figures, 5 table
Air pollution modelling using a graphics processing unit with CUDA
The Graphics Processing Unit (GPU) is a powerful tool for parallel computing.
In the past years the performance and capabilities of GPUs have increased, and
the Compute Unified Device Architecture (CUDA) - a parallel computing
architecture - has been developed by NVIDIA to utilize this performance in
general purpose computations. Here we show for the first time a possible
application of GPU for environmental studies serving as a basement for decision
making strategies. A stochastic Lagrangian particle model has been developed on
CUDA to estimate the transport and the transformation of the radionuclides from
a single point source during an accidental release. Our results show that
parallel implementation achieves typical acceleration values in the order of
80-120 times compared to CPU using a single-threaded implementation on a 2.33
GHz desktop computer. Only very small differences have been found between the
results obtained from GPU and CPU simulations, which are comparable with the
effect of stochastic transport phenomena in atmosphere. The relatively high
speedup with no additional costs to maintain this parallel architecture could
result in a wide usage of GPU for diversified environmental applications in the
near future.Comment: 5 figure
Accelerating moderately stiff chemical kinetics in reactive-flow simulations using GPUs
The chemical kinetics ODEs arising from operator-split reactive-flow
simulations were solved on GPUs using explicit integration algorithms. Nonstiff
chemical kinetics of a hydrogen oxidation mechanism (9 species and 38
irreversible reactions) were computed using the explicit fifth-order
Runge-Kutta-Cash-Karp method, and the GPU-accelerated version performed faster
than single- and six-core CPU versions by factors of 126 and 25, respectively,
for 524,288 ODEs. Moderately stiff kinetics, represented with mechanisms for
hydrogen/carbon-monoxide (13 species and 54 irreversible reactions) and methane
(53 species and 634 irreversible reactions) oxidation, were computed using the
stabilized explicit second-order Runge-Kutta-Chebyshev (RKC) algorithm. The
GPU-based RKC implementation demonstrated an increase in performance of nearly
59 and 10 times, for problem sizes consisting of 262,144 ODEs and larger, than
the single- and six-core CPU-based RKC algorithms using the
hydrogen/carbon-monoxide mechanism. With the methane mechanism, RKC-GPU
performed more than 65 and 11 times faster, for problem sizes consisting of
131,072 ODEs and larger, than the single- and six-core RKC-CPU versions, and up
to 57 times faster than the six-core CPU-based implicit VODE algorithm on
65,536 ODEs. In the presence of more severe stiffness, such as ethylene
oxidation (111 species and 1566 irreversible reactions), RKC-GPU performed more
than 17 times faster than RKC-CPU on six cores for 32,768 ODEs and larger, and
at best 4.5 times faster than VODE on six CPU cores for 65,536 ODEs. With a
larger time step size, RKC-GPU performed at best 2.5 times slower than six-core
VODE for 8192 ODEs and larger. Therefore, the need for developing new
strategies for integrating stiff chemistry on GPUs was discussed.Comment: 27 pages, LaTeX; corrected typos in Appendix equations A.10 and A.1
Accelerating the Gillespie Ï„-Leaping Method Using Graphics Processing Units
The Gillespie Ï„-Leaping Method is an approximate algorithm that is faster than the exact Direct Method (DM) due to the progression of the simulation with larger time steps. However, the procedure to compute the time leap Ï„ is quite expensive. In this paper, we explore the acceleration of the Ï„-Leaping Method using Graphics Processing Unit (GPUs) for ultra-large networks ( reaction channels). We have developed data structures and algorithms that take advantage of the unique hardware architecture and available libraries. Our results show that we obtain a performance gain of over 60x when compared with the best conventional implementations
An investigation of the efficient implementation of Cellular Automata on multi-core CPU and GPU hardware
Copyright © 2015 Elsevier. NOTICE: this is the author’s version of a work that was accepted for publication in Journal of Parallel and Distributed Computing . Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Journal of Parallel and Distributed Computing Vol. 77 (2015), DOI: 10.1016/j.jpdc.2014.10.011Cellular automata (CA) have proven to be excellent tools for the simulation of a wide variety of phenomena in the natural world. They are ideal candidates for acceleration with modern general purpose-graphical processing units (GPU/GPGPU) hardware that consists of large numbers of small, tightly-coupled processors. In this study the potential for speeding up CA execution using multi-core CPUs and GPUs is investigated and the scalability of doing so with respect to standard CA parameters such as lattice and neighbourhood sizes, number of states and generations is determined. Additionally the impact of ‘Activity’ (the number of ‘alive’ cells) within a given CA simulation is investigated in terms of both varying the random initial distribution levels of ‘alive’ cells, and via the use of novel state transition rules; where a change in the dynamics of these rules (i.e. the number of states) allows for the investigation of the variable complexity within.Engineering and Physical Sciences Research Council (EPSRC
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